Project description:The Moutan Cortex Radicis (MCR) has been used as an analgesic, sedative and anti-inflammatory agent. This study investigated the changes in gene expression by MCR treatment when stimulated with lipopolysaccharide (LPS) in cultured human gingival fibroblasts (HGFs) and the gene expression changes by the MCR when challenged with LPS using a microarray chip.

2012-06-28 | GSE38977 | GEO

Loss of B cell Tolerance is TCR Dependent [amplicon-seq]

Project description:We tested orphan TCR autoreactivity using the peptide MHC-TCR chimeric receptor (MCR) co-culture system. In this system, cognate antigen recognition leads to TCR specific NFAT activation in MCR reporter cells expressing a mouse I-Ab MHC class II extracellular domain covalently linked to candidate peptides and an intracellular TCR signaling domain. We used mixed autoimmune bone marrow chimera spleens and kidneys as sources of cDNA to generate a transcriptome-wide library of natural autoantigen peptides . We cloned this cDNA-derived peptide (CDP) autoantigen library into the MCR retroviral backbone and transduced NFAT reporter cells to make a murine autoantigen MCR reporter library (MCR-Lib). We then used this library to screen orphan TCRs identified by scTCR-seq for autoreactivity.

2023-12-29 | GSE229921 | GEO

Comparative genomic profiling and gene expression of Escherichia coli O103:H25 Oslo 2006 outbreak strain

Project description:A food-borne outbreak of haemorrhagic colitis (HC) and HUS caused by E. coli O103:H25 occurred in Norway, 2006. The outbreak included 17 registered cases, of which 10 developed HUS. The aim of this study was to characterize two E. coli O103:H25 isolates from this outbreak. Only one of the isolates carry the stx2 gene (by PCR). Since they have the same typing profile by typing method MLVA, we expect the isolates to have identical gene content except from an Stx2-encoding phage. Therefore, we further investigate whether the Stx2-encoding phage has any impact on the gene expression. Keywords: mixed, gene expression, comparative genomic hybridization Triplicate samples of mRNA from a test strain O157:H7 EDL933 and two outbreak strains - one Stx positive and one stx negative were co-hybridized with genomic DNA from the same strain. Triplicate samples of the Stx positive strain grown at acidic conditions was also co-hybridized with genomic DNA from the Stx positive strain. Genomic DNA for each strain is technical replicates only.

2010-09-01 | E-GEOD-9418 | biostudies-arrayexpress

Project description:Complete genome of mcr-1 encoding isolate NRZ14408

| PRJEB13238 | ENA

Genomic variations define divergence of water/wildlife-associated Campylobacter jejuni niche specialists from common clonal complexes

Project description:Although the major food-borne pathogen Campylobacter jejuni has been isolated from diverse animal, human and environmental sources, our knowledge of genomic diversity in C. jejuni is based exclusively on human or human food-chain-associated isolates. Studies employing multilocus sequence typing have indicated that some clonal complexes are more commonly associated with particular sources. Using comparative genomic hybridization on a collection of 80 isolates representing diverse sources and clonal complexes, we identified a separate clade comprising a group of water/wildlife isolates of C. jejuni with multilocus sequence types uncharacteristic of human food-chain-associated isolates. By genome sequencing one representative of this diverse group (C. jejuni 1336), and a representative of the bank-vole niche specialist ST-3704 (C. jejuni 414), we identified deletions of genomic regions normally carried by human food-chain-associated C. jejuni. Several of the deleted regions included genes implicated in chicken colonization or in virulence. Novel genomic insertions contributing to the accessory genomes of strains 1336 and 414 were identified. Comparative analysis using PCR assays indicated that novel regions were common but not ubiquitous among the water/wildlife group of isolates, indicating further genomic diversity among this group, whereas all ST-3704 isolates carried the same novel accessory regions. While strain 1336 was able to colonize chicks, strain 414 was not, suggesting that regions specifically absent from the genome of strain 414 may play an important role in this common route of Campylobacter infection of humans. We suggest that the genomic divergence observed constitutes evidence of adaptation leading to niche specialization. Data is also available from <ahref=http://bugs.sgul.ac.uk/E-BUGS-95 target=_blank>BuG@Sbase</a>

2011-04-15 | E-BUGS-95 | biostudies-arrayexpress

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